Bug IsoSurface missing libxp6 (was a problem in wmgm2mesh) in container version, now in macapype_env

.github/workflows/check_on_PR.yml

@@ -7,7 +7,6 @@ on:
     branches:
       - master
 
-
 jobs:
   build:
 
@@ -16,7 +15,7 @@ jobs:
     steps:
       - uses: actions/checkout@master
       - name: Set up Python  3.10.5
-        uses: actions/setup-python@v1
+        uses: actions/setup-python@v2
         with:
           python-version:  3.10.5
 

Dockerfile

@@ -9,7 +9,7 @@
 #
 # Timestamp: 2020/12/02 18:33:44 UTC
 
-FROM macatools/macapype_env:latest
+FROM macatools/macapype_env:v0.1.2-spm
 
 USER root
 
@@ -71,4 +71,4 @@ RUN apt-get clean \
 RUN rm -rf \
      /tmp/hsperfdata* \
      /var/*/apt/*/partial \
-     /var/log/apt/term*
+     /var/log/apt/term*

Dockerfile_github

@@ -9,7 +9,7 @@
 #
 # Timestamp: 2020/12/02 18:33:44 UTC
 
-FROM macatools/macapype_env:latest
+FROM macatools/macapype_env:v0.1.2-spm
 
 USER root
 

Dockerfile_macapype_env

@@ -131,22 +131,20 @@ RUN apt-get install -y -q --no-install-recommends \
            netpbm \
            tcsh \
            xfonts-base \
-           xvfb \
-    && curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
-    && dpkg -i /tmp/toinstall.deb \
-    && rm /tmp/toinstall.deb \
-    && curl -sSL --retry 5 -o /tmp/toinstall.deb http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb \
-    && dpkg -i /tmp/toinstall.deb \
-    && rm /tmp/toinstall.deb \
-    && apt-get install -f \
-    && gsl2_path="$(find / -name 'libgsl.so.23' || printf '')" \
-    && if [ -n "$gsl2_path" ]; then \
-         ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; \
-    fi \
-    && ldconfig \
-    && echo "Downloading AFNI ..." \
-    && mkdir -p /opt/afni-latest \
-    && curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
+           xvfb
+
+RUN curl -sSL --retry 5 -o /tmp/toinstall.deb http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb
+RUN dpkg -i /tmp/toinstall.deb
+RUN rm /tmp/toinstall.deb
+RUN apt-get install -f
+RUN gsl2_path="$(find / -name 'libgsl.so.23' || printf '')"
+RUN if [ -n "$gsl2_path" ]; then \
+         ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0";\
+    fi
+RUN ldconfig
+RUN echo "Downloading AFNI ..."
+RUN mkdir -p /opt/afni-latest
+RUN curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
     | tar -xz -C /opt/afni-latest --strip-components 1
 
 ############################################# AFNI IsoSurface requires specifically libXp6

Dockerfile_nomcr

@@ -9,7 +9,7 @@
 #
 # Timestamp: 2020/12/02 18:33:44 UTC
 
-FROM macatools/macapype_env:v0.1.1-nomcr
+FROM macatools/macapype_env:v0.1.2
 
 USER root
 

Dockerfile_testpypi

@@ -9,8 +9,7 @@
 #
 # Timestamp: 2020/12/02 18:33:44 UTC
 
-FROM macatools/macapype_env:latest
-
+FROM macatools/macapype_env:v0.1.2-spm
 USER root
 
 ARG DEBIAN_FRONTEND="noninteractive"

Dockerfile_testpypi_nomcr

@@ -9,7 +9,7 @@
 #
 # Timestamp: 2020/12/02 18:33:44 UTC
 
-FROM macatools/macapype_env:v0.1.1-nomcr
+FROM macatools/macapype_env:v0.1.2
 
 USER root
 

macapype/utils/misc.py

@@ -22,7 +22,7 @@ def print_nii_data(nii_file):
 
 def get_elem(list_elem, index_elem):
     assert isinstance(list_elem, list), 'Error, list_elem should be a list'
-    assert 0 <= index_elem and index_elem < len(list_elem),\
+    assert 0 <= index_elem and index_elem < len(list_elem), \
         ('error with index {}, does not match a list with {} elements'.format(
             index_elem, len(list_elem)))
 
@@ -33,9 +33,8 @@ def get_elem(list_elem, index_elem):
 
 
 def get_index(list_elem, index_elem):
-
     assert isinstance(list_elem, list), 'Error, list_elem should be a list'
-    assert 1 <= index_elem and index_elem < len(list_elem)+1,\
+    assert 1 <= index_elem and index_elem < len(list_elem)+1, \
         ('error with index {}, shoud start at 1 and be smaller than {}'.format(
             index_elem, len(list_elem)+1))
 
@@ -88,7 +87,7 @@ def gzip(unzipped_file):
 
     zipped_file = dest + ".gz"
 
-    assert os.path.exists(zipped_file),\
+    assert os.path.exists(zipped_file), \
         "Error, {} should exists".format(zipped_file)
 
     return zipped_file

macapype/utils/utils_tests.py

@@ -51,7 +51,7 @@ def _download_data_zip(data_zip, name):
 
             return True
 
-    assert op.exists(data_zip),\
+    assert op.exists(data_zip), \
         "Error, data_zip = {} not found ".format(data_zip)
 
     return False